Characterization of the diversity and temporal stability of bacterial communities in human milk

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Hunt, Katherine M ^a   Foster, James A ^a   Forney, Larry J ^a   Schütte, Ursel M E ^a   Beck, Daniel L ^a   Abdo, Zaid ^a   Fox, Lawrence K ^b   Williams, Janet E ^a   McGuire, Michelle K ^b   McGuire, Mark A ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ACTINOMYCES; ADULT; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BRADYRHIZOBIUM; BREAST MILK; CONTROLLED STUDY; CORYNEBACTERIUM; FEMALE; GASTROINTESTINAL TRACT; GEMELLA; GENE AMPLIFICATION; GENE SEQUENCE; GRANULICATELLA; HUMAN; HUMAN EXPERIMENT; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; NORMAL HUMAN; PHYLOGENY; PREVOTELLA; PROPIONIBACTERIUM; PSEUDOMONAS; PYROSEQUENCING; RALSTONIA; ROTHIA; SERRATIA; SPHINGOMONAS; STAPHYLOCOCCUS; STREPTOCOCCUS; TAXONOMY; VEILLONELLA; BACTERIUM; BIODIVERSITY; CLASSIFICATION; LACTATION; MICROBIOLOGY; TIME;

BACTERIA (MICROORGANISMS);

ADULT; BACTERIA; BIODIVERSITY; FEMALE; HUMANS; LACTATION; MILK, HUMAN; PHYLOGENY; TIME FACTORS; YOUNG ADULT;

EID: 79959247053     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021313     Document Type: Article

References (40)

1. Brown KH, Black RE, Lopez de Romaña G, Creed de Kanashiro H, (1989) Infant-feeding practices and their relationship with diarrheal and other diseases in Huascar (Lima), Peru. Pediatrics 83: 31-40.
2. Lopez-Alarcon M, Villalpando S, Fajardo A, (1997) Breast-feeding lowers the frequency and duration of acute respiratory infection and diarrhea in infants under six months of age. J Nutr 127: 436-443.
3. von Kries R, Koletzko B, Sauerwald T, von Mutius E, Barnert D, et al. (1999) Breast feeding and obesity: cross sectional study. Brit Med J 319: 147-150.
4. Gillman MW, Rifas-Shiman SL, Camargo CA, Berkey CS, Frazier AL, et al. (2001) Risk of overweight among adolescents who were breastfed as infants. JAMA 285: 2461-2467.
5. Jensen RG, (1995) Handbook of milk composition San Diego Academic Press.
6. Newburg DS, (2001) Bioactive components of human milk New York Kluwer Academic/Plenum Publishers.
7. Heikella MP, Saris PEJ, (2003) Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J Appl Microbiol 95: 471-478.
8. Martín R, Heilig HGHJ, Zoetendal EG, Jiménez E, Fernández L, et al. (2007) Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res Microbiol 158: 31-37.
9. Martín R, Jiménez E, Heilig H, Fernández L, Marín ML, et al. (2009) Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR. Appl Env Microbiol 75: 965-969.
10. Collado MC, Delgado S, Maldonado A, Rodríguez JM, (2009) Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR. Lett Appl Microbiol 48: 523-528.
11. Gueimonde M, Laitinen K, Salminen S, Isolauri E, (2007) Breast milk: a source of Bifidobacteria for infant gut development and maturation? Neonatology 92: 64-66.
12. Perez PF, Doré J, Leclerc M, Levenez F, Benyacoub J, et al. (2006) Bacterial imprinting of the neanatal immune system: lessons from maternal cells? Pediatrics 119: e724-e732.
13. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R, (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Meth 5: 235-237.
14. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
15. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, et al. (2010) Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA doi:10.1073/pnas.1002611107.
16. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon J, et al. (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
17. Ramsey DT, Kent JC, Owens RA, Hartmann PE, (2004) Ultrasound imaging of milk ejection in the breast of lactating women. Pediatrics 113: 361-367.
18. Nasidze I, Li J, Quinque D, Tang K, Stoneking M, (2009) Global diversity in the human salivary microbiome. Genome Res 19: 636-643.
19. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE, (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721-5732.
20. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and temporal diversity of the human skin microbioime. Science 324: 1190-1192.
21. Gao Z, Tseng C, Pei Z, Blaser MJ, (2007) Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA 104: 2927-2932.
22. Barbosa-Cesnik C, Schwartz K, Foxman B, (2003) Lactation mastitis. JAMA 289: 1609-1612.
23. Foxman B, D'Arcy H, Gillespie B, Bobo JK, Schwartz K, (2002) Lactation mastitis: occurence and medical management among 946 breastfeeding women in the United States. Am J Epidem 155: 103-114.
24. Osterman KL, Rahm V, (2000) Lactation mastitis: bacterial cultivation of breast milk, symptoms, treatment and outcome. J Hum Lact 16: 297-302.
25. Fetherston C, (2001) Mastitis in lactating women: physiology or pathology? Breastfeeding Rev 9: 5-12.
26. National Mastitis Council (1987) Laboratory and Field Handbook on Bovine Mastitis Fort Atkinson, WI W.D. Hoard & Sons.
27. Dohoo IR, Leslie KE, (1991) Evaluation of changes in somatic cell counts as indicators of new intramammary infections. Prev Vet Med 10: 225-237.
28. Yoshioka H, Iseki K, Fujita K, (1983) Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants. Pediatrics 72: 317-322.
29. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, et al. (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53: 685-693.
30. Schwebke JR, (2005) Abnormal vaginal flora as a biological risk factor for acquisition of HIV infection and sexually transmitted diseases. J Infect Dis 192: 1315-1317.
31. Colombo APV, Boches SK, Cotton J, Goodson JM, Kent R, et al. (2009) Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodont 80: 1421-1432.
32. Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, et al. (2007) Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME 1: 121-133.
33. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R, (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucl Acids Res 35: e120.
34. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in open microfabricated high density picoliter reactors. Nature 437: 376-380.
35. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
36. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Gen Biol 8: R143.
37. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2009) Wrinkles in the rare biosphere:pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
38. Huse SM, Welch DM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-1898.
39. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
40. Beck D, Settles M, Foster JA, (2011) OTUBase: an R infrastructure package for taxonomic unit data. Bioinformatics doi:10.1093/bioinformatics/btr196.